Even though the main use case for Bootstrap seems to be for rapid prototyping, any thoughts on using it for a production app (but perhaps custom-themed), instead of rolling a custom design altogether? It seems Bootstrap has matured to the level that it can be used as for most projects with little customizations if any. A lot of what I read in the comments imply that Bootstrap is great at prototyping an app and once that phase is over, you throw it all out and start developing a custom design based on what has been prototyped. Why can't one just stick with Bootstrap and customize it as needed?

Why would you think you can't? Once your app conforms to Bootstrap's markup, you already have a markup/class hierarchy that makes custom styling easy. There's a blog out there that shows Bootstrap sites in the wild and they're customized.